Hi all, I have tried to use the GOtools package, but I have encountered following problem after running the ontoCompare command: [1] "Starting ontoCompare..." Error in if (ncol(results) == 0) results <- NA : argument is of length zero What is the reason for this? My original script is pasted below. THank you: Balazs --------------------------------------- mdr.table.5fu=read.table(?5FU.txt?, header=FALSE, as.is=TRUE) mdr.table.cisplatin=read.table(?cisplatin.txt?, header=FALSE, as.is=TRUE) mdr.table.cyclo=read.table(?cyclophosmphamid.txt?, header=FALSE, as.is=TRUE) mdr.list <- list(fu=mdr.table.5fu, cisplatin=mdr.table.cisplatin, cyclophosphamid=mdr.table.cyclo) mdr.compared<-ontoCompare(mdr.list, probeType ="hgu133a", method = "TIDS", plot = TRUE)

Dear Balazs, This error arises when you pass a vector or a list of vectors as argument to ontoCompare or if the probeType argument doesn't match your data type. OntoCompare is expecting a list or a list of lists, so changing your mdr.list into a list of lists may solve the problem. The probeType argument can be an affy chip or operon (for arrays with Operon oligos). Regards, Agnes -----Original Message----- From: Dr_Gyorffy_Balazs [mailto:zsalab2@yahoo.com] Sent: Monday, August 09, 2004 5:53 AM To: bioconductor@stat.math.ethz.ch Subject: [BioC] GOtools: argument is of length zero Hi all, I have tried to use the GOtools package, but I have encountered following problem after running the ontoCompare command: [1] "Starting ontoCompare..." Error in if (ncol(results) == 0) results <- NA : argument is of length zero What is the reason for this? My original script is pasted below. THank you: Balazs --------------------------------------- mdr.table.5fu=read.table(?5FU.txt?, header=FALSE, as.is=TRUE) mdr.table.cisplatin=read.table(?cisplatin.txt?, header=FALSE, as.is=TRUE) mdr.table.cyclo=read.table(?cyclophosmphamid.txt?, header=FALSE, as.is=TRUE) mdr.list <- list(fu=mdr.table.5fu, cisplatin=mdr.table.cisplatin, cyclophosphamid=mdr.table.cyclo) mdr.compared<-ontoCompare(mdr.list, probeType ="hgu133a", method = "TIDS", plot = TRUE) _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor